US8329659B2 - SAP variants and their use - Google Patents

SAP variants and their use Download PDF

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US8329659B2
US8329659B2 US12/817,535 US81753510A US8329659B2 US 8329659 B2 US8329659 B2 US 8329659B2 US 81753510 A US81753510 A US 81753510A US 8329659 B2 US8329659 B2 US 8329659B2
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amino acid
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W. Scott Willett
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Promedior Inc
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4711—Alzheimer's disease; Amyloid plaque core protein
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P17/00—Drugs for dermatological disorders
    • A61P17/02—Drugs for dermatological disorders for treating wounds, ulcers, burns, scars, keloids, or the like
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P19/00—Drugs for skeletal disorders
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P19/00—Drugs for skeletal disorders
    • A61P19/04—Drugs for skeletal disorders for non-specific disorders of the connective tissue
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P27/00—Drugs for disorders of the senses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P27/00—Drugs for disorders of the senses
    • A61P27/02—Ophthalmic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P27/00—Drugs for disorders of the senses
    • A61P27/02—Ophthalmic agents
    • A61P27/06—Antiglaucoma agents or miotics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P29/00—Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/06—Immunosuppressants, e.g. drugs for graft rejection
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/08—Antiallergic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans

Definitions

  • SAP Serum Amyloid P
  • Molecules bound by SAP are removed from extracellular areas due to the ability of SAP to bind to all three classical Fc ⁇ receptors (Fc ⁇ R), having a particular affinity for Fc ⁇ RII (CD32) and Fc ⁇ RIII (CD16). After receptor binding, SAP and any attached complex are generally internalized and processed by the cell.
  • Fc ⁇ R classical Fc ⁇ receptors
  • CD32 Fc ⁇ RII
  • CD16 Fc ⁇ RIII
  • SAP can be used as a therapeutic agent to treat various disorders, including fibrosis-related disorders, hypersensitivity disorders, autoimmune disorders, mucositis, and inflammatory disorders such as those cause by microbial infection.
  • disorders including fibrosis-related disorders, hypersensitivity disorders, autoimmune disorders, mucositis, and inflammatory disorders such as those cause by microbial infection.
  • Protein therapeutics for treating human disease have revolutionized the health care industry.
  • Many potential therapeutic agents are modified to increase their biological activity, such as plasma half-life, relative to the naturally-derived protein.
  • Recombinant expression technology is usually implemented to produce polypeptides in sufficient quantity.
  • many recombinant systems produce polypeptides having different biological properties than the naturally-derived forms, which may affect the pharmacokinetics, safety, and efficacy of a therapeutic product.
  • the disclosure provides Serum Amyloid P (SAP) variants and SAP oligomers.
  • SAP Serum Amyloid P
  • the disclosure provides an SAP variant comprising five SAP protomers, wherein each of the SAP protomers have an amino acid sequence at least 90% identical to SEQ ID NO: 1, and wherein at least one of the SAP protomers comprises one or more amino acid modifications that alter a biological activity of the SAP variant compared to a corresponding sample of serum-derived human SAP.
  • a variant SAP protomer comprises at least one amino acid modification that is characterized by the presence of one or more variant amino acids relative to SEQ ID NO: 1, the absence of one or more amino acids relative to SEQ ID NO: 1, the coupling of one or more amino acids to a modifying moiety (e.g., a PEG moiety, a dextran moiety, etc.), or a combination thereof.
  • the SAP variant is a variant of a human SAP protein.
  • one or more of the SAP protomers have an amino acid sequence at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 100% identical to SEQ ID NO: 1.
  • SAP variants of the invention have an altered biological activity selected from one or more of increased plasma half-life, increased in vitro stability, or increased in vivo stability.
  • SAP variants of the disclosure are characterized by increased efficiency of manufacturing the SAP protein (e.g., greater yield of the protein product, increased homogeneity of the protein product, increased stability of the protein product).
  • the disclosure provides SAP variants comprising one or more SAP protomers that are substantially free of N-linked or O-linked glycans.
  • an SAP protomer comprises an amino acid modification at position 32 of SEQ ID NO: 1 that inhibits attachment of an N-linked glycan.
  • at least one SAP protomer comprises an amino acid at position 32 of SEQ ID NO: 1 that is not asparagine (N).
  • at least one SAP protomer comprises an aspartate (D), glutamine (Q), or glutamate (E) at position 32 of SEQ ID NO: 1.
  • the disclosure provides SAP variants that are more resistant to protease cleavage than a corresponding sample of serum-derived human SAP.
  • the SAP variants of the disclosure are more resistant to protease cleavage by a serine protease, a threonine proteases, a cysteine protease, an aspartic acid protease, a metalloprotease, a glutamic acid protease, or combinations thereof.
  • the disclosure provides SAP variants that are more resistant to protease cleavage by chymotrypsin, trypsin, Pronase, or combinations thereof.
  • a protease-resistant SAP variant comprises at least one SAP protomer comprises an amino acid at position 144 of SEQ ID NO: 1 that is not phenylalanine (F). In preferred embodiments, a protease-resistant SAP variant comprises at least one SAP protomer comprising an amino acid at position 145 of SEQ ID NO: 1 that is not aspartate (D). In some embodiments, a protease resistant SAP variant comprises at least one SAP protomer comprising an amino acid at position 144 of SEQ ID NO: 1 that is not phenylalanine (F) and an amino acid at position 145 of SEQ ID NO: 1 that is not aspartate (D).
  • a protease-resistant SAP variant comprises at least one SAP protomer comprising a leucine (L), isoleucine (I), valine (V), or alanine (A) at position 144 of SEQ ID NO: 1.
  • a protease-resistant SAP variant comprises at least one SAP protomer comprising a glutamate (E) at position 145 of SEQ ID NO: 1.
  • an SAP variant that is resistant to calcium-dependent autoaggregation comprises at least one SAP protomer comprising an amino acid at position 167 of SEQ ID NO: 1 that is not glutamate (E).
  • an SAP variant that is resistant to calcium-dependent autoaggregation comprises at least one SAP protomer comprising an aspartate (D), asparagine (N), glutamine (Q), alanine (A), or histidine (H) at position 167 of SEQ ID NO: 1.
  • the disclosure provides SAP variants comprises at least one SAP protomer comprising one or more amino acids that are covalently attached to one or more inert polymers.
  • at least one of the inert polymers is a polyethylene glycol (PEG) moiety.
  • one or more of the SAP protomers comprise at least one native or variant (e.g., by amino acid substitution, addition, or deletion) cysteine (C), relative to SEQ ID NO: 1, which has an attached PEG moiety.
  • one or more of the SAP protomers comprise a variant cysteine (C), located at the N-terminus of SEQ ID NO: 1, which has an attached PEG moiety.
  • one or more of the SAP protomers comprise at least one native or variant (Q), relative to SEQ ID NO: 1, which has an attached PEG moiety.
  • one or more of the SAP protomers comprises a glutamine (Q) at position 32 of SEQ ID NO: 1 that has an attached PEG moiety.
  • the SAP variant comprises at least one SAP protomer comprising one or more cysteine (C) residues and one or more glutamine (Q) residues that are attached to a PEG moiety.
  • at least one of the inert polymers is a dextran moiety.
  • one or more of the SAP protomers comprises a native or variant glutamine (Q) residue, relative to SEQ ID NO: 1, which has an attached dextran moiety.
  • one or more of the SAP protomers comprises an native glutamine residue at position 32 of SEQ ID NO: 1 that is has an attached dextran moiety.
  • the SAP variant comprises at least one SAP protomer comprising one or more amino acids attached to a PEG moiety and one or more amino acids attached to a dextran moiety.
  • the disclosure provides an SAP variant comprised of at least two, at least three, at least four, or at least five different variant SAP protomers as described herein.
  • SAP oligomers of the invention may comprise SAP protomers at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 100% identical to the amino acid sequence of SEQ ID NO: 1. Accordingly, SAP oligomers of the invention may comprise at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine or more of the SAP variant protomers as described herein.
  • SAP oligomers of the invention may be comprised of at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine or more different variant SAP protomers as described herein.
  • the crosslinked SAP oligomers of the invention are characterized by one or more of increased plasma half-life, increased in vitro stability, and increased in vivo stability compared to a corresponding sample of SAP isolated from human serum.
  • the SAP oligomers are comprised of SAP pentamers covalently attached through one or more chemical cross-linkers.
  • at least one of the chemical cross-linker is a heterobifunctional agent selected from succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate, m-Maleimidobenzoyl-N-hydroxysuccinimide ester, N-succinimidyl(4-iodoacetyl)aminobenzoate, succinimidyl 4-(p-maleimidophenyl) butyrate, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride, 4-succinimidyloxycarbonyl- ⁇ -methyl- ⁇ (2-pyridyldithio)-toluene, N-succinimidyl 3-(2-pyridyldithio)propionate, or succinimidyl 4-(N
  • At least one of the chemical cross-linkers is a homobifunctional agent selected from disuccinimidyl suberate, bismaleimidohexane, or dimethylpimelimidate-2 HCl.
  • at least one of the chemical cross-linkers is a photoreactive agent selected from bis-( ⁇ -(4-azidosalicylamido)ethyl)disulfide or N-succinimidyl-6-(4′-azido-2′-nitrophenyl-amino) hexanoate.
  • the disclosure provides a pharmaceutical preparation suitable for use in a mammal comprising one or more of the SAP variants and/or covalently crosslinked SAP oligomers.
  • Pharmaceutical preparations of the invention include at least one of the SAP variants and/or SAP oligomers disclosed herein and a pharmaceutically acceptable carrier.
  • the pharmaceutical preparation further comprises an additional active agent.
  • the pharmaceutical preparation is prepared as a sustained release formulation.
  • pharmaceutical preparations of the disclosure are suitable for administration to a patient topically, by injection, by intravenous injection, by inhalation, by continuous depot, or by pump.
  • SAP-responsive disorders or conditions include, but are not limited to, fibrotic or fibroproliferative disorders or conditions, hypersensitivity disorders or conditions, autoimmune disorders or conditions, and mucositis.
  • SAP variant and/or oligomer of the invention may be administered to a patient topically, by injection, by intravenous injection, by inhalation, by continuous depot or pump, or a combination thereof.
  • the SAP variant and/or oligomer of the invention is administered conjointly with one or more additional active agents.
  • the SAP variants and/or oligomers are formulated to be administered conjointly.
  • the SAP variants and/or oligomers may be conjointly administered as separate or in combined formulations.
  • the SAP variants and/or oligomers may be administered simultaneously or at different dosing schedules.
  • FIG. 1 An SAP variant comprising an amino acid substitution E167Q, relative to the sequence of SEQ ID NO: 1, is more resistant to calcium-mediated aggregation than a corresponding sample of unmodified recombinant human SAP (rhSAP). Incremental amounts of calcium was added a solution comprising SAP, and the amount of SAP aggregation was observed by measuring the absorbance of the solution at 600 nm in a spectrophotometer.
  • FIG. 3 SAP variants E167Q and N32D, relative to the sequence of SEQ ID NO: 1, are at least as active as a corresponding sample of unmodified recombinant human SAP (rhSAP).
  • rhSAP unmodified recombinant human SAP
  • PMBCs Peripheral Blood Mononuclear Cells
  • MDC Macrophage Derived Chemokine
  • FIG. 5 Depicts a chemical reaction that covalent attaches PEG to rhSAP.
  • FIG. 6 Pegylated-rhSAP was purified from reaction components by anion exchange chromatography. Fractions from the chromatography column were pooled and concentrated before analysis by SDS-PAGE.
  • Serum amyloid P (“SAP”) is a naturally-occurring serum protein in mammals and is a member of the pentraxin family of structurally related proteins. It is produced in the liver as a 125,000 Dalton glycoprotein and has a physiological half-life of 24 hours in serum.
  • SAP is composed of five identical subunits or “protomers” which are non-covalently associated in a disc-like molecule. SAP protomers non-covalently associate with each other via two “protomer interfaces”. Protomer interface 1 from subunit 1 associates with protomer interface 2 from subunit 2.
  • Protomer interface 1 from subunit 2 associates with protomer interface 2 from subunit 3, etc.
  • SAP aggregates and may precipitate as the amyloid P component, which is a normal constituent of glomerular basement membrane as well as human dermis, cervix, testis, and placenta tissues.
  • amyloid P component which is a normal constituent of glomerular basement membrane as well as human dermis, cervix, testis, and placenta tissues.
  • Fibrocytes, fibrocyte precursors, myofibroblast precursors, and hematopoetic monocyte precursors belong to a distinct population of fibroblast-like cells derived from peripheral blood monocytes. These cells can migrate to sites of tissue injury to promote angiogenesis and wound healing.
  • SAP was shown to inhibit fibrocyte, fibrocyte precursor, myofibroblast precursor, and/or hematopoetic monocyte precursor differentiation at levels similar to that of serum.
  • plasma depleted of SAP has a reduced ability to inhibit differentiation of monocytes into fibrocytes, fibrocyte precursors, myofibroblast precursors, and/or hematopoetic monocyte precursors.
  • serum from subjects with rheumatoid arthritis, sceleroderma, mixed connective tissue diseases, and certain systemic fibrotic diseases have reduced potency for inhibiting fibrocyte, fibrocyte precursor, myofibroblast precursor, and/or hematopoetic monocyte precursor differentiation in vitro.
  • SAP serum levels of SAP are significantly lower in some subjects with these disorders than is observed for health subjects. These results indicate that abnormally low levels of SAP may augment pathological processes leading to fibrosis and suggests SAP may be useful as a therapeutic agent to inhibit fibrosis in chronic inflammatory conditions. Recently, it has been suggested that SAP can be used as a therapeutic agent to treat various other disorders, including fibrosis-related disorders, hypersensitivity disorders, autoimmune disorders, mucositis, and inflammatory disorders such as those caused by microbial infection. See, for example, U.S. patent application Ser. Nos. 11/707,333, 12/217,617 12/720,845, and 12/720,847.
  • Polypeptides are susceptible to denaturation or enzymatic degradation in the blood, liver or kidney. Due to the low stability of some polypeptides, it has been required to administer polypeptide drugs in a sustained frequency to a subject in order to maintain an effective plasma concentration of the active substance. Moreover, since polypeptide drugs are usually administrated by infusion, frequent injection of polypeptide drugs may cause considerable discomfort to a subject. Thus, there have been many studies to develop polypeptide drugs that have an increased circulating half-life in the blood, while maintaining a high pharmacological efficacy. Accordingly, a primary object of the present disclosure is to provide SAP variants, compositions, pharmaceutical preparations and formulations having a prolonged in vivo half-life compared to human SAP. Advantages of increased plasma half-life include, but are not limited to, reducing the amount and/or frequency of dosing.
  • compositions of therapeutic peptides preferably have a shelf-life of several years in order to be suitable for common use.
  • peptide compositions are inherently unstable due to sensitivity towards chemical and physical degradation. Examples of chemical degradation include change of covalent bonds, including but not limited to, oxidation, hydrolysis, racemization, or crosslinking Examples of physical degradation include conformational changes relative to the native structure of the peptide, which may lead to aggregation, precipitation, or adsorption of the polypeptide to surfaces.
  • a further object of the present disclosure is to provide SAP variants, compositions, pharmaceutical preparations and formulations that have a prolonged shelf-life, or rather increased in vitro stability, compared to human SAP.
  • SAP variants of the disclosure are characterized by increased efficiency of manufacturing the SAP protein (e.g., greater yield of the protein product, increased homogeneity of the protein product, increased stability of the protein product), particularly for in vivo use (e.g., as a therapeutic agent).
  • an element means one element or more than one element.
  • treatment refers to obtaining a desired pharmacologic and/or physiologic effect.
  • the effect may be prophylactic in terms of completely or partially preventing a disorder or symptom thereof and/or may be therapeutic in terms of a partial or complete cure for a disorder and/or adverse affect attributable to the disorder.
  • Treatment covers any treatment of a disease in a mammal, particularly in a human, and includes: (a) increasing survival time; (b) decreasing the risk of death due to the disease; (c) decreasing the risk of a disease from occurring in a subject which may be predisposed to the disease but has not yet been diagnosed as having it; (d) inhibiting the disease, i.e., arresting its development (e.g., reducing the rate of disease progression); and (e) relieving the disease, i.e., causing regression of the disease.
  • a therapeutic that “inhibits” or “prevents” a disorder or condition is a compound that, in a statistical sample, reduces the occurrence of the disorder or condition in the treated sample relative to an untreated control sample, or delays the onset or reduces the severity of one or more symptoms of the disorder or condition relative to the untreated control sample.
  • subject and “patient” refer to animals including mammals, such as humans.
  • mammal includes primates, domesticated animals including dogs, cats, sheep, cattle, horses, goats, pigs, mice, rats, rabbits, guinea pigs, captive animals such as zoo animals, and wild animals.
  • tissue refers to an organ or set of specialized cells such as skin tissue, lung tissue, kidney tissue, and other types of cells.
  • therapeutic effect is art-recognized and refers to a local or systemic effect in animals, particularly mammals, and more particularly humans caused by a pharmacologically active substance.
  • therapeutically effective amount means that amount of such a substance that produces some desired local or systemic effect at a reasonable benefit/risk ratio applicable to any treatment.
  • the therapeutically effective amount of such substance will vary depending upon the subject and disease condition being treated, the weight and age of the subject, the severity of the disease condition, the manner of administration and the like, which can readily be determined by one of ordinary skill in the art.
  • certain compositions described herein may be administered in a sufficient amount to produce a desired effect at a reasonable benefit/risk ratio applicable to such treatment.
  • nucleic acid refers to a polynucleotide such as deoxyribonucleic acid (DNA), and, where appropriate, ribonucleic acid (RNA).
  • DNA deoxyribonucleic acid
  • RNA ribonucleic acid
  • the term should also be understood to include, as equivalents, analogs of either RNA or DNA made from nucleotide analogs, and, as applicable to the embodiment being described, single-stranded (such as sense or antisense) and double-stranded polynucleotide.
  • purified protein refers to a preparation of a protein or proteins that are preferably isolated from, or otherwise substantially free of, other proteins normally associated with the protein(s) in a cell or cell lysate.
  • substantially free of other cellular proteins or “substantially free of other contaminating proteins” is defined as encompassing individual preparations of each of the proteins comprising less than 20% (by dry weight) contaminating protein, and preferably comprises less than 5% contaminating protein.
  • Functional forms of each of the proteins can be prepared as purified preparations by using a cloned gene as is well known in the art.
  • purified it is meant that the indicated molecule is present in the substantial absence of other biological macromolecules, such as other proteins (particularly other proteins which may substantially mask, diminish, confuse or alter the characteristics of the component proteins either as purified preparations or in their function in the subject reconstituted mixture).
  • the term “purified” as used herein preferably means at least 80% by dry weight, more preferably in the range of 85% by weight, more preferably 95-99% by weight, and most preferably at least 99.8% by weight, of biological macromolecules of the same type present (but water, buffers, and other small molecules, especially molecules having a molecular weight of less than 5000, can be present).
  • pure as used herein preferably has the same numerical limits as “purified” immediately above.
  • half-life or “plasma half-life”, as used herein in the context of administering a peptide drug to a subject, is defined as the time required for plasma concentration of a drug in a subject to be reduced by one half. Further explanation of “half-life” is found in Pharmaceutical Biotechnology (1997, D F A Crommelin and R D Sindelar, eds., Harwood Publishers, Amsterdam, pp 101 120).
  • SAP variant proteins Serum Amyloid P (SAP) variant proteins.
  • SAP variant is intended to refer to an SAP protein comprising five SAP subunits or “protomers”.
  • an SAP variant comprises at least one SAP protomer having one or more amino acid modifications (i.e., a variant SAP protomer) that modify at least one biological activity of the SAP protein.
  • amino acid modifications include, but are not limited to, the presence of one or more variant amino acids relative to the sequence of SEQ ID NO: 1 (e.g., amino acid substitution or addition), the absence of one or more native amino acids relative to the sequence of SEQ ID NO: 1 (e.g., amino acid deletion), the coupling of one or more amino acids to a modifying moiety (e.g., a PEG moiety, a dextran moiety, etc.), or a combination thereof.
  • an SAP protomer comprises at least one variant amino acid, relative to SEQ ID NO: 1, and at least one amino acid coupled to a modifying moiety.
  • SAP variants of the invention are characterized by an altered biological activity compared to a corresponding sample of serum-derived human SAP.
  • an SAP variant of the disclosure is characterized by an altered biological activity selected from one or more of increased plasma half-life, increased in vivo stability, increased in vitro stability, or increased manufacturing efficiency.
  • SAP protomer is intended to refer to a polypeptide that is at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identical to the SAP protomer exemplified by SEQ ID NO. 1. Accordingly, the term “SAP protomer” encompasses fragments and fusion proteins comprising any of the preceding. In preferred aspects, SAP variants of the disclosure are human SAP proteins. Generally, an SAP protomer will be designed to be soluble in aqueous solutions at biologically relevant temperatures, pH levels, and osmolarity.
  • an SAP variant may be comprised of at least two, at least three, at least four, or five identical SAP protomers or, alternatively, comprised of at least two, at least three, at least four, or at least five identical or different variant SAP protomers.
  • at least one, at least two, at least three, or at least four of the SAP protomers have 100% sequence identity to SEQ ID NO: 1.
  • an SAP variant comprises at least one variant SAP protomer that confers one or more altered biological activity as described herein.
  • Post-translational modifications may be effected in vivo and/or in vitro and include, but are not limited to, processing (e.g., signal sequence removal, pro-peptide maturation, etc.) and chemical modification (e.g., glycosylation, pegylation, etc.) of the translated SAP polypeptides.
  • processing e.g., signal sequence removal, pro-peptide maturation, etc.
  • chemical modification e.g., glycosylation, pegylation, etc.
  • the invention also provides SAP protomers sharing a specified degree of sequence identity or similarity to an SAP polypeptide.
  • the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes).
  • at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95% or more of the length of a reference sequence (e.g., human SAP) is aligned for comparison purposes.
  • the amino acid residues at corresponding amino acid positions are then compared.
  • amino acid “identity” is equivalent to amino acid “homology”.
  • the percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
  • the percent identity between two amino acid sequences is determined using the Needleman and Wunsch (J Mol. Biol. (48):444-453 (1970)) algorithm which has been incorporated into the GAP program in the GCG software package (available at http://www.gcg.com).
  • the following parameters are used in the GAP program: either a Blossom 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6.
  • the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package (Devereux, J., et al., Nucleic Acids Res.
  • Exemplary parameters include using an NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6.
  • the percent identity between two amino acid sequences is determined using the algorithm of E. Myers and W. Miller (CABIOS, 4:11-17 (1989)), which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.
  • Another embodiment for determining the best overall alignment between two amino acid sequences can be determined using the FASTDB computer program based on the algorithm of Brutlag et al. (Comp. App. Biosci., 6:237-245 (1990)).
  • a sequence alignment the query and subject sequences are both amino acid sequences. The result of said global sequence alignment is presented in terms of percent identity.
  • amino acid sequence identity is performed using the FASTDB computer program based on the algorithm of Brutlag et al. (Comp. App. Biosci., 6:237-245 (1990)).
  • SAP polypeptides i.e., protomers
  • the reference sequence corresponds to the amino acid sequence of SEQ ID NO: 1.
  • such polypeptides may have a certain percentage of amino acid residues which are not identical to a reference sequence.
  • the non-identical residues have similar chemical properties to the residues to which they are not identical. Groups that have similar properties include the following amino acids: E, D, N, and Q; H, K, and R; Y, F and W; I, L, V, M, C, and A; and S, T, C, P, and A.
  • the residues which are not identical are those which are not evolutionarily conserved between the reference sequence and an orthologous sequence in at least one evolutionarily related species, such as in species within the same order.
  • the amino acids that may be mutated in a preferred embodiment are those that are not conserved between the reference sequence and the orthologous sequence in another mammal species.
  • a polypeptide used in a method of the present invention is said to comprise an amino acid sequence that is at least 90% identical to human SAP (SEQ ID NO:1), then said polypeptide may have non-identical residues to those positions in which the human SAP and that of another mammal differ.
  • SAP polypeptides (i.e., protomers) sharing at least 90% identity with SEQ ID NO:1 include polypeptides having conservative substitutions in these areas of divergence. Typically seen as conservative substitutions are the replacements, one for another, among the aliphatic amino acids Ala, Val, Leu, and Ile, interchange of the hydroxyl residues Ser and Thr, exchange of the acidic residues Asp and Glu, substitution between the amide residues Asn and Gln, exchange of the basic residues Lys and Arg and replacements among the aromatic residues Phe, Tyr. Additional guidance concerning which amino acid changes are likely to be phenotypically silent can be found in Bowie et al., Science 247:1306-1310 (1990).
  • an SAP variant i) comprises one or more protomers that are least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% identical to SEQ ID NO: 1, ii) has one or more of the following features compared to a corresponding sample of serum-derived human SAP: increased plasma half-life, increased in vitro stability, increased in vivo stability, or increased manufacturing efficiency.
  • amino acids of an SAP protomer may be mutated by adding one or more specified amino acid residues, deleting one or more specified amino acid residues, or substituting one or more specified amino acid residues.
  • Methods for mutating or chemically modifying SAP polypeptides are described in the following sections.
  • the serum half-life of an SAP variant is at least one, at least two, at least three, at least four, at least five, at least ten, or at least twenty days or more.
  • Methods for pharmacokinetic analysis and determination of half-life and in vivo stability will be familiar to those skilled in the art. Details may be found in Kenneth, A et al: Chemical Stability of Pharmaceuticals: A Handbook for Pharmacists and in Peters et al, Pharmacokinetc analysis: A Practical Approach (1996).
  • one method for determining in vivo stability involves administering an SAP variant to an animal and measuring the concentration of the SAP variant within the plasma of the animal at regular intervals after administration.
  • the pharmacokinetic profile i.e. plasma concentration of SAP over time
  • another SAP protein e.g., a corresponding sample of serum-derived human SAP.
  • SAP variants of the disclosure are more stable than an otherwise identical composition of human SAP under identical conditions.
  • the disclosed compositions have a shelf-life, or in vitro, stability at least two times, at least three times, at least four times, or at least five times or more as long as a corresponding sample human SAP.
  • Many methods for measure in vitro stability are know in the art, including, for example, measuring protein stability by SDS-PAGE, Western blot, RP-HPLC, AEX-HPLC, LC-MS, or N-terminal sequencing.
  • SAP variants of the invention have an altered or similar bioactivity compared to a corresponding sample of serum-derived human SAP.
  • Bioactivity of an SAP variant may be determined, for example, by determining the IC 50 for inhibiting the differentiation of monocytes into fibrocytes in vitro.
  • the IC 50 of an SAP variant is less than 1 ⁇ 2, less than 1 ⁇ 3, less than 1 ⁇ 4, less than 1/10, or less than 1/100 that of a corresponding sample of wild-type SAP isolated from human serum.
  • PBMCs Peripheral Blood Mononuclear Cells
  • PBMCs or monocytes suitable for use in these methods may be obtained from various tissue culture lines.
  • suitable cells for fibrocyte differentiation assays may be obtained from any biological sample that contains PBMC or monocyte cells.
  • the biological sample may be obtained from serum, plasma, healthy tissue, or fibrotic tissue.
  • fibrocyte differentiation assays are conducted by incubating PBMC or monocyte cells in media with various concentrations of a SAP polypeptide to determine the degree of fibrocyte differentiation.
  • the concentration of SAP can range from 0.0001 ⁇ g/mL to 1 mg/ml, and in some embodiments is 0.001 ⁇ g/mL, 1.0 ⁇ g/mL, 5 ⁇ g/mL, 10 ⁇ g/mL, 15 ⁇ g/mL, 20 ⁇ g/mL, 25 ⁇ g/mL, 30 ⁇ g/mL, 35 ⁇ g/mL, 40 ⁇ g/mL, 45 ⁇ g/mL, 50 ⁇ g/mL, 100 ⁇ g/mL, 200 ⁇ g/mL, 300 ⁇ g/mL, or 500 ⁇ g/mL
  • the media can be supplemented with between 1-100 ng/ml hMCSF; the preferred concentration of hMCSF being 25 ng/mL
  • the indication that PBMC and monocytes have differentiated into fibrocytes can be determined by one skilled in the art.
  • fibrocytes are morphologically defined as adherent cells with an elongated spindle-shape and the presence of an oval nucleus.
  • cells are fixed and stained with Hema 3 before enumerating fibrocytes by direct counting, e.g., using an inverted microscope.
  • the amount of fibrocyte differentiation is interpreted by one skilled in the art as an indication of a cell's responsiveness to SAP. As indicated by the examples of the disclosure, a greater suppression of fibrocyte differentiation indicates a greater degree of SAP responsiveness.
  • An alternative method of measuring fibrocyte differentiation involves determining the expression of fibrocyte-specific cell surface markers or secreted factors,e.g., cytokines (such as IL-1ra, ENA-78/CXCL-5, PAI-1), fibronecctin, collagen-1, Macrophage Derived Chemokine).
  • cytokines such as IL-1ra, ENA-78/CXCL-5, PAI-1
  • fibronecctin such as IL-1ra, ENA-78/CXCL-5, PAI-1
  • fibronecctin such as collagen-1, Macrophage Derived Chemokine.
  • the disclosure provides SAP variants that are more resistant to protease cleavage than a corresponding sample of serum-derived human SAP.
  • An SAP variant of the invention may be resistant to protease cleavage from any number of proteases including serine proteases, threonine proteases, cysteine proteases, aspartic acid proteases, metalloproteases, and glutamic acid proteases.
  • an SAP variant is more resistant to cleavage by chymotrypsin, trypsin, or Pronase.
  • the protease resistant SAP variant has an increased plasma half-life compared to a corresponding sample of serum-derived human SAP.
  • Methods for measuring proteolytic cleavage include, but are not limited to, analyzing protease-treated samples of a protein (e.g., an SAP variant and a serum-derived human SAP standard) by SDS-PAGE, Western blot, RP-HPLC, AEX-HPLC, LC-MS, or N-terminal sequencing.
  • a protein e.g., an SAP variant and a serum-derived human SAP standard
  • SDS-PAGE Western blot
  • RP-HPLC e.g., a serum-derived human SAP standard
  • RP-HPLC e.g., AEX-HPLC
  • LC-MS e.g., N-terminal sequencing.
  • Other examples of protease cleavage assays are within the purview of a person skilled in the art and are exemplified in Kinoshita CM, et al., Protein Science 1:700-709 (1992). Therefore, SAP variants of the invention can readily be assa
  • an SAP protomer comprises an amino acid modification at position 144 and/or position 145 of SEQ ID NO: 1, resulting in an SAP variant that is more resistant to protease cleavage.
  • an SAP protomer comprises a variant amino acid at position 144 of SEQ ID NO: 1.
  • SAP variants more resistant to protease cleavage may have a leucine (L), isoleucine (I), valine (V), alanine (A), or glutamine (Q) residue at amino acid position 144 of SEQ ID NO: 1.
  • AN SAP protomer may also comprise, independently or in combination with, a variant amino acid at position 145 of SEQ ID NO: 1.
  • Variant SAP protomers of the disclosure may comprise a glutamate (E) at position 145 at SEQ ID NO: 1.
  • an SAP variant comprises one or more promoters that are i) at least 85%, at least 90%, at least 95%, at least 96% at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 1, and ii) comprise one or more of the following amino acid substitutions F144L, F144I, F144V, F144A, F144G, D145E relative to SEQ ID NO: 1. Any of the aforementioned SAP protomers that are resistant to protease cleavage may further comprise any of the other amino acid modifications described herein.
  • an SAP variant having increased metal-binding comprises one or more SAP protomers with a variant amino acid at position 145 of SEQ ID NO: 1.
  • SAP variants characterized by increased metal-binding may have a glutamate (E), glutamine (Q), histindine (H), alanine (A), glycine (G) amino acid at position 145 of SEQ ID NO: 1.
  • an SAP variant demonstrate increased metal-binding to calcium as compared to a corresponding sample of serum-derived human SAP.
  • Calcium binding constants for an SAP protein can be measured by a variety of methods, including those exemplified in Calcium-binding Protein Protocols: methods and techniques by Hans J. Vogel, Contributor Hans J. Vogel, Published by Humana Press, 2002.
  • calcium binding constants for an SAP protein can be measured by equilibrium dialysis using a range of calcium concentrations followed by Scatchard plot analysis. (See, for example Segel, I. H., Enzyme Kinetics 1975, Wiley-Interscience Publisher, p 218-19).
  • Equilibrium dialysis may be performed using either radioactive isotopes of calcium or calcium sensitive electrodes to quantify free calcium levels.
  • Calcium binding constants may also be determined by titrating calcium into a solution of SAP in the presence of a chromophoric chelator (5,5′-dibromo-1,2-bis(2aminophenoxy) ethane-N,N,N′,N′-tetraacetic acid (Linse, S, Helmbersson, A. Forsen, S, 1991 JBC 266:13 pp. 8050-8054).
  • Isothermal Titration Calorimetry can also be used to measure calcium binding affinities (Wiseman, T., Williston, S., Brandts, J.
  • SAP variants characterized by increased metal-binding can be compared to a corresponding sample of serum-derived human SAP for changes in proteolytic stability (e.g., digestion with chymotrypsin in the presence and absence of calcium), in vitro bioactivity and or pharmacokinetics, as well as biophysical characterization methods (e.g., RP-HPLC, SE-HPLC, SDS-PAGE, LC-MS).
  • proteolytic stability e.g., digestion with chymotrypsin in the presence and absence of calcium
  • biophysical characterization methods e.g., RP-HPLC, SE-HPLC, SDS-PAGE, LC-MS.
  • an SAP variant comprises one or more SAP protomers that are i) at least 85%, at least 90%, at least 95%, at least 96% at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 1, and ii) comprising one or more of the following amino acid substitutions: D145E, D145Q, D145H, D145A, or D145G. Any of the aforementioned SAP protomers that demonstrate increased metal-binding may further comprise any of the other amino acid modifications described herein.
  • an SAP variant of the disclosure is more resistant to calcium-dependent autoaggregation than a corresponding sample of serum-derived human SAP.
  • an SAP variant resistant to calcium-dependent autoaggregation comprises one or more SAP protomers comprising a variant amino acid at position 167 of SEQ ID NO: 1.
  • an SAP variant resistant to calcium-dependent autoaggregation comprises an aspartate (D), asparagines (N), glutamine (Q), alanine (A), or histidine (H) at position 167 of SEQ ID NO: 1.
  • Aggregation of SAP can be determined by any number of known methods including gel filtration chromatography and dynamic light scattering (see Ho, et. al., J Biol Chem 280:31999-32008 (2005)). Therefore, SAP variants of the invention can readily be assayed for relative resistance to aggregation in comparison to a corresponding sample of another SAP protein, e.g., a sample of serum-derived human SAP.
  • an SAP variant comprises one or more SAP protomers that are at least 85%, at least 90%, at least 95%, at least 96% at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 1, and ii) comprises one or more one or more of the following amino acid substitutions: E167D, E167N, E167Q E167A, E167H. Any of the aforementioned SAP protomers that are resistant to autoaggregation may further comprise any of the other amino acid modifications described herein.
  • N-linked refers to the attachment of the carbohydrate moiety to the side chain of an asparagine residue.
  • the tripeptide sequences asparagine-X-serine and asparagine-X-threonine, where X is any amino acid except proline, are the recognition sequences for enzymatic attachment of a carbohydrate moiety to the asparagine side chain.
  • O-linked glycosylation refers to the attachment of sugar moieties (e.g., N-aceytlgalactosamine, galactose, or xylose) to a hydroxyamino acid, most commonly on a serine or threonine residue.
  • sugar moieties e.g., N-aceytlgalactosamine, galactose, or xylose
  • the disclosure provides an SAP variant comprising at least one SAP protomer that is substantially free of glycans.
  • substantially free is meant that at least about 25% (e.g., at least about 27%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95%, or at least about 99%) of the amino acids of the SAP protomer are non-glycosylated.
  • an SAP protomer, or SAP variant is free of any glycan-linked structure.
  • SAP protomers of the disclosure have been modified to inhibit attachment of N-linked glycans, O-linked glycans or both N- and O-linked glycans.
  • Removal of N-linked glycosylation sites on an SAP variant is accomplished by modifying (e.g., by amino acid deletion, addition or substitution) the amino acid sequence of one or more of the SAP protomers such that the protomer lacks one or more of the above-described tripeptide sequences (for N-linked glycosylation sites).
  • the alteration may also include the deletion or substitution of one or more serine or threonine residues of the SAP protomer.
  • an SAP variant comprises at least one SAP protomer comprising a variant amino acid at position 32, 33, and/or 34 of SEQ ID NO: 1.
  • a variant SAP protomer comprises an aspartate (D), glutamine (Q), or glutamate (E) at position 32 of SEQ ID NO: 1.
  • a variant SAP protomer may also comprise, independently or in combination with, a proline at position 33 of SEQ ID NO: 1.
  • an SAP variant comprises one or more protomers that are i) at least 85%, at least 90%, at least 95%, at least 96% at least 97%, at least 98% or at least 99% identical to SEQ ID NO: 1, and ii) comprises one or more of the following amino acid substitutions: N32D, N32Q, N32E, 33P. Any of the aforementioned SAP protomers that are substantially free of glycans may further comprise any of the other amino acid modifications described herein.
  • an SAP variant of the invention comprises one or more SAP protomers comprising one or more amino acid covalently attached to one or more inert polymers.
  • An inert polymer attached to an SAP protomer may be of any effective molecular weight and may be branched or unbranched.
  • Polymers used in the instant invention include, but are not limited to, (a) dextran and dextran derivatives, including dextran sulfate, cross-linked dextrin, and carboxymethyl dextrin; (b) cellulose and cellulose derivatives, including methylcellulose and carboxymethyl cellulose; (c) starch, cyclodextrins and dextrins, and derivatives thereof; (d) polyalkylene glycol and derivatives thereof, including PEG, mPEG, PEG homopolymers, polypropylene glycol homopolymers, copolymers of ethylene glycol with propylene glycol, wherein said homopolymers and copolymers are unsubstituted or substituted at one end with an alkyl group; (e) heparin and fragments of heparin; (f) polyvinyl alcohol and polyvinyl ethyl ethers; (g) polyvinylpyrrolidone; (h) ⁇ , ⁇ -poly(
  • the disclosure provides an SAP variant comprising one or more SAP protomers comprising at least one amino acid covalently attached to a polyethylene glycol moiety.
  • the molecular weight of a polyethylene glycol moiety is between about 1 kDa and about 100 kDa (the term “about” indicating that in preparations of polyethylene glycol, some molecules will weigh more, some less, than the stated molecular weight). Other sizes may be used, depending on the desired therapeutic profile (e.g., the duration of sustained release desired, the degree or lack of antigenicity, etc.).
  • the polyethylene glycol may have an average molecular weight of at least 1, at least 20, or at least 40 kDa.
  • the polyethylene glycol may have a branched structure, and branched polyethylene glycols are described, for example, in U.S. Pat. No. 5,643,575; Morpurgo et al., Appl. Biochem. Biotechnol. 56:59-72 (1996); Vorobjev et al., Nucleosides Nucleotides 18:2745-2750 (1999); and Caliceti et al., Bioconjug. Chem. 10:638-646 (1999).
  • Polyethylene glycol moieties may be attached to an SAP variant with consideration of effects on catalytic or targeting portions.
  • the disclosure provides an SAP variant comprising one or more SAP protomers comprising at least one amino acid covalently attached to a dextran moiety.
  • the molecular weight of a dextran moiety attached to the SAP protomer is generally between about 1 kDa and about 250 kDa (the term “about” indicating that in preparations of dextran conjugates, some molecules will weigh more, some less, than the stated molecular weight). Other sizes may be used, depending on the desired therapeutic profile (e.g., the duration of sustained release desired, the degree or lack of antigenicity, etc.).
  • the dextran may have an average molecular weight of at least 1, at least 20, or at least 40 kDa.
  • SAP may be conjugated to dextran or a dextran derivative including dextran sulfate, p-aminoethyl cross-linked dextran, and carboxymethyl dextran.
  • the disclosure provides SAP oligomers comprising two or more SAP pentamers.
  • the SAP oligomers are covalently-crosslinked pentamers, i.e., via protomer-protomer crosslinks
  • SAP pentamers are cross-linked using one or more heterobifunctional cross-linkers, which can be used to link proteins in a stepwise manner.
  • Heterobifunctional cross-linkers provide the ability to design more specific coupling methods for conjugating proteins, thereby reducing the occurrences of unwanted side reactions such as homo-protein polymers.
  • a wide variety of heterobifunctional cross-linkers are known in the art.
  • SCC succinimid
  • cross-linking agents having N-hydroxysuccinimide moieties can be obtained as the N-hydroxysulfosuccinimide analogs, which generally have greater water solubility.
  • those cross-linking agents having disulfide bridges within the linking chain can be synthesized instead as the alkyl derivatives so as to reduce the amount of linker cleavage in vivo.
  • DSS Disuccinimidyl suberate
  • BMH bismaleimidohexane
  • DMP dimethylpimelimidate-2 HCl
  • BASED bis-( ⁇ -(4-azidosalicylamido)ethyl)disulfide
  • BASED bis-( ⁇ -(4-azidosalicylamido)ethyl)disulfide
  • SANPAH N-succinimidyl-6-(4′-azido-2′-nitrophenyl-amino) hexanoate
  • heterobifunctional cross-linkers contain the primary amine reactive group, N-hydroxysuccinimide (NHS), or its water soluble analog N-hydroxysulfosuccinimide (sulfo-NHS).
  • NHS N-hydroxysuccinimide
  • sulfo-NHS water soluble analog N-hydroxysulfosuccinimide
  • Thiols are also particularly useful reactive groups as part of a heterobifunctional cross-linker
  • Common thiol reactive groups include maleimides, halogens, and pyridyl disulfides.
  • Maleimides react specifically with free sulfhydryls (cysteine residues) in minutes, under slightly acidic to neutral (pH 6.5-7.5) conditions.
  • Halogens iodoacetyl functions
  • a third component of the heterobifunctional cross-linker is the spacer arm or bridge.
  • the bridge is the structure that connects the two reactive ends. The most apparent feature of the bridge is its effect on steric hindrance. In some instances, a longer bridge can more easily span the distance necessary to link two complex biomolecules.
  • Preparing protein-protein conjugates using heterobifunctional reagents is a two-step process involving the amine reaction and the sulfhydryl reaction, and such processes are generally well known in the art. See, e.g., Partis et al. (1983) J. Pro. Chem. 2:263); Ellman et al. (1958) Arch. Biochem. Biophys. 74:443; Riddles et al. (1979) Anal. Biochem. 94:75); Blattler et al. (1985) Biochem 24:1517).
  • the disclosure provides a covalently crosslinked SAP oligomer comprising at least two SAP pentamers, wherein each of the SAP pentamers comprises five SAP protomers.
  • SAP oligomers of the invention may be comprised of SAP protomers at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 100% identical to the amino acid sequence of SEQ ID NO:1.
  • SAP oligomers of the invention may comprise at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine or more of the variant SAP protomers described herein.
  • SAP oligomers of the invention may be comprised of at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine or more different variant SAP protomers as described herein.
  • a crosslinked SAP oligomer of the invention is characterized by one or more of increased plasma half-life, increased in vitro stability, and increased in vivo stability compared to a corresponding sample of SAP isolated from human serum.
  • the crosslinked SAP oligomers have one or more of the following characteristics as compared to serum-derived human SAP: increased resistance to protease, increased resistance to calcium-mediated autoaggregation, and increased metal ion-binding.
  • SAP variants of the disclosure may comprise at least one protomer having one or more amino acid alterations that modify at least one biological activity of the SAP protein.
  • methods of generating amino acid alterations include, but are not limited to, mutating at least one amino acid of SEQ ID NO: 1 (e.g., deletion of one or more amino acids, addition of one or more amino acids, or substitution of one or more amino acids), chemically modifying one or more amino acids of SEQ ID NO: 1 (e.g., attaching one or more inert polypeptides to an amino acid of SEQ ID NO: 1), or a combination thereof.
  • variant SAP protomers of the invention may be generated using random mutagenesis techniques, directed mutagenesis techniques, directed evolution, or combination thereof.
  • Variant SAP protomers may be generated using techniques that introduce random or directed mutations in the coding sequence of a nucleic acid.
  • the nucleic acid is then expressed in a desired expression system, and the resulting peptide is assessed for properties of interest, e.g., resistance to autoaggregation, resistance to protease cleavage, increased metal-ion binding, increased serum half-live, increased in vitro half-life, increased in vivo half-life.
  • reduced Taq polymerase fidelity is used to introduce random mutations into a cloned fragment of DNA (Leung et al., 1989, Technique 1:11 15).
  • the DNA region to be mutagenized is amplified using PCR under conditions that reduce the fidelity of DNA synthesis by Taq DNA polymerase, e.g., by using an altered dGTP/dATP ratio and by adding Mn 2+ to the PCR reaction.
  • the pool of amplified DNA fragments are inserted into appropriate cloning vectors to provide random mutant libraries.
  • Saturation mutagenesis allows for the rapid introduction of a large number of single base substitutions into cloned DNA fragments (Mayers et al., 1985, Science 229:242).
  • This technique includes generation of mutations, e.g., by chemical treatment or irradiation of single-stranded DNA in vitro and synthesis of a complementary DNA strand.
  • the mutation frequency can be modulated by modulating the severity of the treatment, and essentially all possible base substitutions can be obtained. Because this procedure does not involve a genetic selection for mutant fragments, both neutral substitutions as well as those that alter function, are obtained. Furthermore, the distribution of point mutations is not biased toward conserved sequence elements.
  • a library of nucleic acid homologs can also be generated from a set of degenerate oligonucleotide sequences. Chemical synthesis of a degenerate oligonucleotide sequences can be carried out in an automatic DNA synthesizer, and the synthetic genes may then be ligated into an appropriate expression vector. The synthesis of degenerate oligonucleotides is known in the art (see for example, Narang, S A (1983) Tetrahedron 39:3; Itakura et al. (1981) Recombinant DNA, Proc 3rd Cleveland Sympos. Macromolecules, ed. A G Walton, Amsterdam: Elsevier pp. 273 289; Itakura et al.
  • Variant SAP protomers may also be generated using “directed evolution” techniques. These strategies are different from traditional random mutagenesis procedures because they involve subjecting the nucleic acid sequence encoding the peptide of interest to recursive rounds of mutation, screening and amplification.
  • the diversity in the nucleic acids obtained is generated by mutation methods that randomly create point mutations in the nucleic acid sequence.
  • the point mutation techniques include, but are not limited to, “error-prone PCRTM”(Caldwell and Joyce, 1994; PCR Methods Appl. 2: 28 33; and Ke and Madison, 1997, Nucleic Acids Res. 25: 3371 3372), repeated oligonucleotide-directed mutagenesis (Reidhaar-Olson et al., 1991, Methods Enzymol. 208:564 586), and any of the aforementioned methods of random mutagenesis.
  • mutator genes Another method of creating diversity upon which directed evolution can act is the use of mutator genes.
  • the nucleic acid of interest is cultured in a mutator cell strain the genome of which typically encodes defective DNA repair genes (U.S. Pat. No. 6,365,410; Selifonova et al., 2001, Appl. Environ. Microbiol. 67:3645 3649; Long-McGie et al., 2000, Biotech. Bioeng. 68:121 125; see, Genencor International Inc, Palo Alto Calif.).
  • Achieving diversity using directed evolution techniques may also be accomplished using saturation mutagenesis along with degenerate primers (Gene Site Saturation MutagenesisTM, Diversa Corp., San Diego, Calif.).
  • degenerate primers designed to cover the length of the nucleic acid sequence to be diversified are used to prime the polymerase in PCR reactions.
  • each codon of a coding sequence for an amino acid may be mutated to encode each of the remaining common nineteen amino acids.
  • This technique may also be used to introduce mutations, deletions and insertions to specific regions of a nucleic acid coding sequence while leaving the rest of the nucleic acid molecule untouched. Procedures for the gene saturation technique are well known in the art, and can be found in U.S. Pat. No. 6,171,820.
  • Variant SAP protomers may also be generated using the techniques of gene-shuffling, motif-shuffling, exon-shuffling, and/or codon-shuffling (collectively referred to as “DNA shuffling”).
  • DNA shuffling techniques are may be employed to modulate the activities of peptides useful in the invention and may be used to generate peptides having altered activity. See, generally, U.S. Pat. Nos. 5,605,793; 5,811,238; 5,830,721; 5,834,252; and 5,837,458, and Stemmer et al. (1994, Nature 370(6488):389 391); Crameri et al.
  • DNA shuffling involves the assembly of two or more DNA segments by homologous or site-specific recombination to generate variation in the polynucleotide sequence.
  • DNA shuffling has been used to generate novel variations of human immunodeficiency virus type 1 proteins (Pekrun et al., 2002, J. Virol. 76(6):2924 35), triazine hydrolases (Raillard et al. 2001, Chem Biol 8(9):891 898), murine leukemia virus (MLV) proteins (Powell et al. 2000, Nat Biotechnol 18(12):1279 1282), and indoleglycerol phosphate synthase (Merz et al. 2000, Biochemistry 39(5):880 889).
  • DNA shuffling was developed to generate biomolecular diversity by mimicking natural recombination by allowing in vitro homologous recombination of DNA (Stemmler, 1994, Nature 370: 389 391; and Stemmler, 1994, PNAS 91: 10747 10751).
  • a population of related genes is fragmented and subjected to recursive cycles of denaturation, rehybridization, followed by the extension of the 5′ overhangs by Taq polymerase. With each cycle, the length of the fragments increases, and DNA recombination occurs when fragments originating from different genes hybridize to each other.
  • DNA shuffling methods have advantages over random point mutation methods in that direct recombination of beneficial mutations generated by each round of shuffling is achieved and there is therefore a self-selection for improved phenotypes of peptides.
  • the techniques of DNA shuffling are well known to those in art.
  • exon shuffling exons or combinations of exons that encode specific domains of peptides are amplified using chimeric oligonucleotides. The amplified molecules are then recombined by self-priming PCR assembly (Kolkman and Stemmler, 2001, Nat. Biotech. 19:423 428).
  • RACHITT random chimeragenesis on transient templates
  • staggered extension process (StEP), thermocycling with very abbreviated annealing/extension cycles is employed to repeatedly interrupt DNA polymerization from flanking primers (Zhao et al., 1998, Nat. Biotechnol. 16: 258 261).
  • CLERY in vitro family shuffling is combined with in vivo homologous recombination in yeast (Abecassis et al., 2000, Nucleic Acids Res. 28:E88).
  • Maxygen Redwood City, Calif.
  • this company will perform customized directed evolution procedures including gene shuffling and selection on a peptide family of choice.
  • Optigenix, Inc. offers the related service of plasmid shuffling.
  • Optigenix uses families of genes to obtain mutants therein having new properties.
  • the nucleic acid of interest is cloned into a plasmid in an Aspergillus expression system.
  • the DNA of the related family is then introduced into the expression system and recombination in conserved regions of the family occurs in the host. Resulting mutant DNAs are then expressed and the peptide produced therefrom are screened for the presence of desired properties and the absence of undesired properties.
  • the desired peptides expressed by mutated genes are screened for characteristics of interest.
  • the “candidate” genes are then amplified and pooled for the next round of DNA shuffling.
  • the screening procedure used is highly dependant on the peptide that is being “evolved” and the characteristic of interest. Characteristics such as peptide stability, biological activity, antigenicity, among others can be selected using procedures that are well known in the art.
  • the above techniques of mutation and selection can be combined with each other and with additional procedures to generate the best possible variant SAP protomer useful in the methods of the invention.
  • the invention is not limited to any one method for the generation of SAP variants, and should be construed to encompass any and all of the methodology described herein.
  • a procedure for introducing specified point mutations into a nucleic acid sequence may be performed initially, followed by recursive rounds of DNA shuffling, selection and amplification.
  • the initial introduction of point mutations may be used to introduce diversity into a gene population where it is lacking, and the following round of DNA shuffling and screening will select for advantageous point mutations.
  • the disclosure provides methods for chemically modifying one or more amino acids of an SAP protomer.
  • methods for attaching inert polymers to a polypeptide including, but not limited to, using cyanogen bromide (alkylation) and dialdehyde coupling chemistry and periodate oxidation.
  • many methods for pegylating amino acids have been described in the art.
  • U.S. Pat. No. 4,088,538 discloses an enzymatically active polymer-enzyme conjugate of an enzyme covalently bound to PEG.
  • 4,496,689 discloses a covalently attached complex of ⁇ -1 protease inhibitor with a polymer such as PEG or methoxypoly(ethylene glycol) (“mPEG”).
  • mPEG methoxypoly(ethylene glycol)
  • Abuchowski et al. J. Biol. Chem. 252: 3578 (1977) discloses the covalent attachment of mPEG to an amine group of bovine serum albumin
  • U.S. Pat. No. 4,414,147 discloses a method of rendering interferon less hydrophobic by conjugating it to an anhydride of a dicarboxylic acid, such as poly(ethylene succinic anhydride).
  • PCT WO 87/00056 discloses conjugation of PEG and polyoxyethylated polyols to such proteins as interferon- ⁇ , interleukin-2 and immunotoxins.
  • EP 154,316 discloses and claims chemically modified lymphokines, such as IL-2 containing PEG bonded directly to at least one primary amino group of the lymphokine.
  • U.S. Pat. No. 4,055,635 discloses pharmaceutical compositions of a water-soluble complex of a proteolytic enzyme linked covalently to a polymeric substance such as a polysaccharide. Another mode of attaching PEG to peptides is through the non-specific oxidation of glycosyl residues on a peptide.
  • the oxidized sugar is utilized as a locus for attaching a PEG moiety to the peptide.
  • WO 94/05332 discloses the use of a hydrazine- or amino-PEG to add PEG to a glycoprotein.
  • the glycosyl moieties are randomly oxidized to the corresponding aldehydes, which are subsequently coupled to the amino-PEG.
  • an SAP protomer is modified by the introduction of a “free” cysteine residues (i.e., cysteines that are not involved in disulfide bonds) to which PEG can be attached using well described malaimide chemistry.
  • a “free” cysteine residues i.e., cysteines that are not involved in disulfide bonds
  • Modified SAP variants are provided, wherein polymer conjugation sites are introduced via variant cysteine residues.
  • the cysteine residue may be substituted for one or more native SAP amino acid residues or by adding one or more cysteines to an SAP polypeptide.
  • a cysteine residue is introduced at position ⁇ 1 of SEQ ID NO: 1 (i.e., added to the N-terminus of the polypeptide).
  • a cysteine residue in introduced by the substitution of the native amino acid a position 32 of SEQ ID NO: 1 for a cysteine residue.
  • the introduced cysteine is pegylated.
  • the polypeptide may be treated with a reducing agent, such as dithiothreitol (DDT) prior to pegylation.
  • DDT dithiothreitol
  • the reducing agent is subsequently removed by any conventional method, such as by desalting.
  • Conjugation of PEG to a cysteine residue typically takes place in a suitable buffer at pH 6-9 at temperatures varying from 4° C. to 25° C. for periods up to about 16 hours.
  • activated PEG polymers for coupling to cysteine residues include the following linear and branched PEGs, including but not limited to, vinylsulfone-PEG (PEG-VS), such as vinylsulfone-mPEG (mPEG-VS); orthopyridyl-disulfide-PEG (PEG-OPSS), such as orthopyridyl-disulfide-mPEG (MPEG-OPSS); and maleimide-PEG (PEG-MAL), such as maleimide-mPEG (mPEG-MAL) and branched maleimide-mPEG2 (mPEG2-MAL).
  • PEG-VS vinylsulfone-PEG
  • PEG-OPSS orthopyridyl-disulfide-PEG
  • MPEG-OPSS orthopyridyl-disulfide-mPEG
  • PEG-MAL maleimide-PEG
  • mPEG-MAL maleimide-mPEG
  • transglutaminase glutamyl-peptide ⁇ -glutamyltransferase; EC 2.3.2.13
  • This enzyme catalyzes the calcium-dependent acyl addition to a primary amine wherein the gamma-carboxamide group of peptide-bound glutamine residue is the acyl donor and the primary amine is the acyl acceptor and amine donor.
  • a transglutaminase reaction is therefore employed to covalently and site-specifically conjugate SAP to a polymer, such as PEG or dextran through a Gln residue that is capable of acting as a transglutaminase amine acceptor.
  • the transglutaminase amine acceptor in SAP may be an native or introduced (i.e., variant) Gln residue.
  • glutamine repeats have been shown to enhance the acceptor properties of each glutamine residue in the repeat, and the accessibility of glutamine residues has also been shown to be important in determining their ability to function as transglutaminase substrates (Kahlem, P. et al. Proc. Natl. Acad. Sci. USA 1996, 93, 14580-14585).
  • the SAP variant comprises an N32Q mutation, introducing a transglutaminase amine acceptor.
  • the SAP variant comprises the amino acid sequence at least 70, 80, 85, 90, 95, 98, or 100% identical to SEQ ID NO: 2 (wherein X is any amino acid, A is 3 to 20, and Y is 1 to 10):
  • Y is 1. In some embodiments, Y is 2. In some embodiments, the SAP variant is conjugated to PEG via a transglutaminase amine acceptor. In some embodiments, the SAP variant is conjugated to dextran via a transglutaminase amine acceptor.
  • SAP variants and SAP covalently crosslinked oligomers described herein may be produced in bacterial cells, insect cells, yeast, fungal cells, or mammalian cells including, for example, human cells.
  • the host cell may be in a live subject or may be isolated from a subject, e.g., in a cell culture, tissue sample, cell suspension, etc.
  • Other suitable host cells are known to those skilled in the art.
  • expression vectors for producing SAP protomers.
  • expression vectors are contemplated which include a nucleotide sequence encoding an SAP protomer, wherein the coding sequence is operably linked to at least one transcriptional regulatory sequence.
  • Regulatory sequences for directing expression of SAP protomers are art-recognized and are selected by a number of well understood criteria. Exemplary regulatory sequences are described in Goeddel; Gene Expression Technology: Methods in Enzymology, Academic Press, San Diego, Calif. (1990). For instance, any of a wide variety of regulatory sequences that control the expression of a DNA sequence when operatively linked to it may be used in these vectors to express DNA sequences encoding SAP protomers.
  • the design of the expression vector may depend on such factors as the choice of the target host cell to be transformed. Moreover, the vector's copy number, the ability to control that copy number and the expression of any other protein encoded by the vector, such as antibiotic markers, should also be considered.
  • the disclosure also provides a host cell transfected with a recombinant gene in order to express an SAP protomer.
  • the host cell may be any prokaryotic or eukaryotic cell.
  • an SAP protomer may be expressed in bacterial cells such as E. coli , insect cells, yeast, or mammalian cells. Other suitable host cells are known to those skilled in the art.
  • a host cell transfected with an expression vector encoding an SAP protomer of the invention can be cultured under appropriate conditions to allow expression of the polypeptide to occur.
  • the SAP protomer may be secreted, by inclusion of a secretion signal sequence, and isolated from a mixture of cells and medium containing the protein.
  • the SAP protomer may be retained cytoplasmically and the cells harvested, lysed and the protomer isolated.
  • a cell culture includes host cells, media and other byproducts. Suitable media for cell culture are well known in the art.
  • the proteins can be isolated from cell culture medium, host cells, or both using techniques known in the art for purifying proteins, including ion-exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, and immunoaffinity purification with antibodies specific for particular epitopes of the protein.
  • a coding sequence for an SAP protomer can be used to produce a recombinant form of the protein via microbial or eukaryotic cellular processes.
  • Expression vehicles for production of a recombinant protein include plasmids and other vectors.
  • suitable vectors for the expression of SAP protomers include plasmids of the types: pBR322-derived plasmids, pEMBL-derived plasmids, pEX-derived plasmids, pBTac-derived plasmids and pUC-derived plasmids for expression in prokaryotic cells, such as E. coli.
  • YEp24, YIp5, YEp51, YEp52, pYES2, and YRp17 are cloning and expression vehicles useful in the introduction of genetic constructs into S. cerevisiae (see, for example, Broach et al., (1983) in Experimental Manipulation of Gene Expression, ed. M. Inouye Academic Press, p. 83, incorporated by reference herein).
  • These vectors can replicate in E. coli due the presence of the pBR322 ori, and in S. cerevisiae due to the replication determinant of the yeast 2 micron plasmid. Autotrophic selection or counterselection is often used in yeast.
  • drug resistance markers such as ampicillin, can be used in bacteria.
  • Mammalian expression vectors may contain both prokaryotic sequences to facilitate the propagation of the vector in bacteria, and one or more eukaryotic transcription units that are expressed in eukaryotic cells.
  • the pcDNAI/amp, pcDNAI/neo, pRc/CMV, pSV2gpt, pSV2neo, pSV2-dhfr, pTk2, pRSVneo, pMSG, pSVT7, pko-neo and pHyg derived vectors are examples of mammalian expression vectors suitable for transfection of eukaryotic cells.
  • vectors are modified with sequences from bacterial plasmids, such as pBR322, to facilitate replication and drug resistance selection in both prokaryotic and eukaryotic cells.
  • bacterial plasmids such as pBR322
  • derivatives of viruses such as the bovine papilloma virus (BPV-1), or Epstein-Barr virus (pHEBo, pREP-derived and p205) can be used for transient expression of proteins in eukaryotic cells.
  • BBV-1 bovine papilloma virus
  • pHEBo Epstein-Barr virus
  • pREP-derived and p205 Epstein-Barr virus
  • examples of other viral (including retroviral) expression systems can be found below in the description of gene therapy delivery systems.
  • the various methods employed in the preparation of the plasmids and transformation of host organisms are well known in the art.
  • baculovirus expression systems include pVL-derived vectors (such as pVL1392, pVL1393 and pVL941), pAcUW-derived vectors (such as pAcUW1), and pBlueBac-derived vectors (such as the beta-gal containing pBlueBac III).
  • pVL-derived vectors such as pVL1392, pVL1393 and pVL941
  • pAcUW-derived vectors such as pAcUW1
  • pBlueBac-derived vectors such as the beta-gal containing pBlueBac III.
  • MRC 5 cells MRC 5 cells; FS4 cells; a human hepatoma line (Hep G2); and myeloma or lymphoma cells (e.g. Y0, J558L, P3 and NS0 cells) (see U.S. Pat. No. 5,807,715).
  • Hep G2 human hepatoma line
  • myeloma or lymphoma cells e.g. Y0, J558L, P3 and NS0 cells
  • production of SAP protomers may be achieved using in vitro translation systems.
  • In vitro translation systems are, generally, a translation system which is a cell-free extract containing at least the minimum elements necessary for translation of an RNA molecule into a protein.
  • An in vitro translation system typically comprises at least ribosomes, tRNAs, initiator methionyl-tRNAMet, proteins or complexes involved in translation, e.g., eIF2, eIF3, the cap-binding (CB) complex, comprising the cap-binding protein (CBP) and eukaryotic initiation factor 4F (eIF4F).
  • CBP cap-binding protein
  • eIF4F eukaryotic initiation factor 4F
  • in vitro translation systems examples include eukaryotic lysates, such as rabbit reticulocyte lysates, rabbit oocyte lysates, human cell lysates, insect cell lysates and wheat germ extracts. Lysates are commercially available from manufacturers such as Promega Corp., Madison, Wis.; Stratagene, La Jolla, Calif.; Amersham, Arlington Heights, Ill.; and GIBCO/BRL, Grand Island, N.Y. In vitro translation systems typically comprise macromolecules, such as enzymes, translation, initiation and elongation factors, chemical reagents, and ribosomes. In addition, an in vitro transcription system may be used.
  • eukaryotic lysates such as rabbit reticulocyte lysates, rabbit oocyte lysates, human cell lysates, insect cell lysates and wheat germ extracts. Lysates are commercially available from manufacturers such as Promega Corp., Madison, Wis.; Stratagene, La Jolla
  • Such systems typically comprise at least an RNA polymerase holoenzyme, ribonucleotides and any necessary transcription initiation, elongation and termination factors.
  • In vitro transcription and translation may be coupled in a one-pot reaction to produce proteins from one or more isolated DNAs.
  • SAP variants can be purified using fractionation and/or conventional purification methods and media Ammonium sulfate precipitation and acid or chaotrope extraction may be used for fractionation of samples.
  • Exemplary purification steps may include hydroxyapatite, size exclusion, FPLC and reverse-phase high performance liquid chromatography.
  • Suitable anion exchange media include derivatized dextrans, agarose, cellulose, polyacrylamide, specialty silicas, and the like.
  • PEI, DEAE, QAE and Q derivatives are suitable, including, for example, DEAE Fast-Flow Sepharose (Pharmacia, Piscataway, N.J.).
  • Exemplary chromatographic media include those media derivatized with phenyl, butyl, or octyl groups, such as Phenyl-Sepharose FF (Pharmacia), Toyopearl butyl 650 (Toso Haas, Montgomeryville, Pa.), Octyl-Sepharose (Pharmacia) and the like; or polyacrylic resins, such as Amberchrom CG 71 (Toso Haas) and the like.
  • Suitable solid supports include glass beads, silica-based resins, cellulosic resins, agarose beads, cross-linked agarose beads, polystyrene beads, cross-linked polyacrylamide resins and the like that are insoluble under the conditions in which they are to be used. These supports may be modified with reactive groups that allow attachment of proteins by amino groups, carboxyl groups, sulfhydryl groups, hydroxyl groups and/or carbohydrate moieties. Examples of coupling chemistries include cyanogen bromide activation, N-hydroxysuccinimide activation, epoxide activation, sulfhydryl activation, hydrazide activation, and carboxyl and amino derivatives for carbodiimide coupling chemistries.
  • the disclosure provides methods for treating an SAP-responsive disorder in a patient by administering a therapeutically effective amount of an SAP variant or SAP oligomer of the invention to a patient in need thereof.
  • the dosage and frequency of treatment can be determined by one skilled in the art and will vary depending on the symptoms, age and body weight of the patient, and the nature and severity of the disorder to be treated or prevented.
  • an SAP variant or SAP oligomer is administered to a patient once or twice per day, once or twice per week, once or twice per month, or just prior to or at the onset of symptoms.
  • the SAP-responsive disorder is a hypersensitivity disorder such as those mediated by Th1 or Th2 responses.
  • a hypersensitivity disorder such as those mediated by Th1 or Th2 responses.
  • the use of SAP as a therapeutic treatment for hypersensitivity disorders is also described in U.S. Provisional Application No. 61/209,795, which is hereby incorporated by reference.
  • Hypersensitivity-related disorders that may be amenable to treatment with SAP include, but are not limited to, allergic rhinitis, allergic sinusitis, allergic conjunctivitis, allergic bronchoconstriction, allergic dyspnea, allergic increase in mucus production in the lungs, atopic eczema, dermatitis, urticaria, anaphylaxis, pneumonitis, and allergic-asthma.
  • an SAP variant or SAP oligomer of the invention may be used to treat allergen-specific immune responses, such as anaphylaxis, to various antigens, including, but not limited to, antimicrobials (e.g., cephalosporins, sulfonamides, penicillin and other ⁇ -lactams), anticonvulsants (e.g., phenytoin, phenobarital, carbamazepine, dapsone, allopurinal, and minocycline), chemotheraputics (e.g., taxanes, platinum compounds, asparaginases, and epipodophyllotoxins), heparin, insulin, protamine, aspirin and other non-steroidal anti-inflammatory drugs, muscle relaxants (e.g., succinylcholine, atracurium, vecuronium, and pancuronium), induction agents (e.g., barbiturates, etomidate, propofol), narcotics
  • Autoimmune related disorders that may be amenable to treatment with SAP include, but are not limited to, type I diabetes, multiple sclerosis, rheumatoid arthritis, psoriatic arthritis, autoimmune myocarditis, pemphigus, myasthenia gravis, Hashimoto's thyroiditis, Graves' disease, Addison's disease, autoimmune hepatitis, chronic Lyme arthritis, familial dilated cardiomyopathy, juvenile dermatomyositis, polychondritis, Sjogren's syndrome, psoriasis, juvenile idiopathic arthritis, inflammatory bowel disease, systemic lupus erythematosus, chronic obstructive pulmonary disease, and graft-versus-host disease.
  • the SAP-responsive disorder is a mucositis.
  • the use of SAP as a therapeutic treatment for mucositis is also described in U.S. application Ser. No. 12/217,614, which is hereby incorporated by reference.
  • Methods of the invention may be useful for treating oral, esophageal, and gastrointestinal mucositis, as well as gastric and duodenal ulcers, or erosions of the stomach and esophagus.
  • an SAP variant or SAP oligomer of the invention may be used to treat an inflammatory disease.
  • the inflammatory disease may be a viral, bacterial, fungal, or parasitic infection.
  • the use of SAP as a therapeutic treatment for viral infection has also been described in U.S. Pat. No. 6,406,698 and in PCT Application WO1997/026906, which are both hereby incorporated by reference.
  • the disclosure provides pharmaceutical preparations comprising one or more SAP therapeutic agents (i.e., SAP variants and SAP oligomers) formulated for administration.
  • SAP therapeutic agents i.e., SAP variants and SAP oligomers
  • the therapeutic agents of the invention may be formulated in a conventional manner using one or more physiologically acceptable carriers or excipients.
  • therapeutic agents and their physiologically acceptable salts and solvates may be formulated for administration by, for example, injection (e.g. SubQ, IM, IP), inhalation or insufflation (either through the mouth or the nose) or oral, buccal, sublingual, transdermal, nasal, parenteral or rectal administration.
  • therapeutic agents may be administered locally, at the site where the target cells are present, i.e., in a specific tissue, organ, or fluid (e.g., blood, cerebrospinal fluid, tumor mass, etc.).
  • the present invention further provides use of any SAP variant or SAP oligomer of the invention in the manufacture of a medicament for the treatment or prevention of a disorder or a condition, as described herein, in a patient, for example, the use of an SAP variant or SAP oligomer in the manufacture of medicament for the treatment of a disorder or condition described herein.
  • any SAP variant or SAP oligomer of the invention may be used to make a pharmaceutical preparation for the use in treating or preventing a disease or condition described herein.
  • Therapeutic agents can be formulated for a variety of modes of administration, including systemic and topical or localized administration. Techniques and formulations generally may be found in Remington's Pharmaceutical Sciences, Meade Publishing Co., Easton, Pa.
  • parenteral administration injection is preferred, including intramuscular, intravenous, intraperitoneal, and subcutaneous.
  • the compounds can be formulated in liquid solutions, preferably in physiologically compatible buffers such as Hank's solution or Ringer's solution.
  • the compounds may be formulated in solid form and redissolved or suspended immediately prior to use. Lyophilized forms are also included.
  • the therapeutic agents can be administered to cells by a variety of methods know to those familiar in the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other vehicles, such as hydrogels, cyclodextrins, biodegradable nanocapsules, and bioadhesive micro spheres.
  • the pharmaceutical compositions may take the form of, for example, tablets, lozenges, or capsules prepared by conventional means with pharmaceutically acceptable excipients such as binding agents (e.g., pregelatinised maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulo se); fillers (e.g., lactose, microcrystalline cellulose or calcium hydrogen phosphate); lubricants (e.g., magnesium stearate, talc or silica); disintegrants (e.g., potato starch or sodium starch glycolate); or wetting agents (e.g., sodium lauryl sulphate).
  • binding agents e.g., pregelatinised maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulo se
  • fillers e.g., lactose, microcrystalline cellulose or calcium hydrogen phosphate
  • lubricants e.g., magnesium stearate, talc or silica
  • Liquid preparations for oral administration may take the form of, for example, solutions, syrups or suspensions, or they may be presented as a dry product for constitution with water or other suitable vehicle before use.
  • Such liquid preparations may be prepared by conventional means with pharmaceutically acceptable additives such as suspending agents (e.g., sorbitol syrup, cellulose derivatives or hydrogenated edible fats); emulsifying agents (e.g., lecithin or acacia); non-aqueous vehicles (e.g., almond oil, oily esters, ethyl alcohol or fractionated vegetable oils); and preservatives (e.g., methyl or propyl-p-hydroxybenzoates or sorbic acid).
  • the preparations may also contain buffer salts, flavoring, coloring and sweetening agents as appropriate.
  • Preparations for oral administration may be suitably formulated to give controlled release of the active compound.
  • therapeutic agents may be conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebulizer, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas.
  • a suitable propellant e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas.
  • a suitable propellant e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas.
  • a suitable propellant e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas.
  • the pharmaceutical compounds can also be administered by intranasal or intrabronchial routes including insufflation, powders, and aerosol formulations (for examples of steroid inhalants, see Rohatagi (1995) J. Clin. Pharmacol. 35:1187-1193; Tjwa (1995) Ann Allergy Asthma Immunol. 75:107-111).
  • aerosol formulations can be placed into pressurized acceptable propellants, such as dichlorodifluoromethane, propane, nitrogen, and the like. They also may be formulated as pharmaceuticals for non-pressured preparations such as in a nebulizer or an atomizer Typically, such administration is in an aqueous pharmacologically acceptable buffer.
  • SAP variants or SAP oligomers of the invention may be formulated for parenteral administration by injection, e.g., by bolus injection or continuous infusion.
  • Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multi-dose containers, with an added preservative.
  • the compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.
  • the active ingredient may be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.
  • SAP variants or SAP oligomers of the invention may also be formulated as a depot preparation.
  • Such long-acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection.
  • therapeutic agents may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.
  • Controlled release formula also includes patches.
  • the compounds described herein can be formulated for delivery to the central nervous system (CNS) (reviewed in Begley, Pharmacology & Therapeutics 104: 29-45 (2004)).
  • CNS central nervous system
  • Conventional approaches for drug delivery to the CNS include: neurosurgical strategies (e.g., intracerebral injection or intracerebroventricular infusion); molecular manipulation of the agent (e.g., production of a chimeric fusion protein that comprises a transport peptide that has an affinity for an endothelial cell surface molecule in combination with an agent that is itself incapable of crossing the blood-brain-barrier in an attempt to exploit one of the endogenous transport pathways of the blood-brain-barrier); pharmacological strategies designed to increase the lipid solubility of an agent (e.g., conjugation of water-soluble agents to lipid or cholesterol carriers); and the transitory disruption of the integrity of the BBB by hyperosmotic disruption (resulting from the infusion of a mannitol solution into the carotid
  • SAP variants or SAP oligomers of the invention are incorporated into a topical formulation containing a topical carrier that is generally suited to topical drug administration and comprising any such material known in the art.
  • the topical carrier may be selected so as to provide the composition in the desired form, e.g., as an ointment, lotion, cream, microemulsion, gel, oil, solution, or the like, and may be comprised of a material of either naturally occurring or synthetic origin. It is preferable that the selected carrier not adversely affect the active agent or other components of the topical formulation.
  • suitable topical carriers for use herein include water, alcohols and other nontoxic organic solvents, glycerin, mineral oil, silicone, petroleum jelly, lanolin, fatty acids, vegetable oils, parabens, waxes, and the like.
  • compositions may comprise from about 0.00001 to 100% such as from 0.001 to 10% or from 0.1% to 5% by weight of one or more of the SAP variants or SAP oligomers described herein.
  • the active agent is present in an amount in the range of approximately 0.25 wt. % to 75 wt. % of the formulation, preferably in the range of approximately 0.25 wt. % to 30 wt. % of the formulation, more preferably in the range of approximately 0.5 wt. % to 15 wt. % of the formulation, and most preferably in the range of approximately 1.0 wt. % to 10 wt. % of the formulation.
  • Conditions of the eye can be treated or prevented by, e.g., systemic, topical, intraocular injection of therapeutic agents, or by insertion of a sustained release device that releases therapeutic agents.
  • SAP variants or SAP oligomers of the invention may be delivered in a pharmaceutically acceptable ophthalmic vehicle, such that the compound is maintained in contact with the ocular surface for a sufficient time period to allow the compound to penetrate the corneal and internal regions of the eye, as for example the anterior chamber, conjunctiva, posterior chamber, vitreous body, aqueous humor, vitreous humor, cornea, iris/ciliary, lens, choroid/retina and sclera.
  • the pharmaceutically acceptable ophthalmic vehicle may, for example, be an ointment, vegetable oil or an encapsulating material.
  • the compounds may be injected directly into the vitreous and aqueous humour.
  • the compounds may be administered systemically, such as by intravenous infusion or injection, for treatment of the eye.
  • Therapeutic agents described herein may be stored in oxygen-free environment according to methods in the art.
  • an SAP variant or SAP oligomer is administered in a time release formulation, for example in a composition which includes a slow release polymer.
  • An SAP variant or SAP oligomer can be prepared with carriers that will protect against rapid release. Examples include a controlled release vehicle, such as a polymer, microencapsulated delivery system, or bioadhesive gel.
  • prolonged delivery of an SAP variant or SAP oligomer may be achieved by including in the composition agents that delay absorption, for example, aluminum monostearate hydrogels and gelatin.
  • nucleic acid compounds Methods for delivering nucleic acid compounds are known in the art (see, e.g., Akhtar et al., 1992, Trends Cell Bio., 2, 139; and Delivery Strategies for Antisense Oligonucleotide Therapeutics, ed. Akhtar, 1995; Sullivan et al., PCT Publication No. WO 94/02595). These protocols can be utilized for the delivery of virtually any nucleic acid compound.
  • FIG. 1 demonstrates that the rhSAP variant E167Q is significantly more resistant to calcium-mediated aggregation that the wild-type rhSAP.
  • an in vitro bioassay was used to determine the relative activity of the rhSAP variant E167Q.
  • monocyte-enriched Peripheral Blood Mononuclear Cells PBMCs
  • PBMCs Peripheral Blood Mononuclear Cells
  • MDC Macrophage Derived Chemokine
  • SAP samples and standards were initially diluted to a concentration of 1.0 mg/mL in Supplemented FibroLife Media.
  • SAP standards were serially diluted to generate working standard concentrations of 60, 30, 20, 13.4, 8.8, 6.0, 3.0, 1.5, and 0.75 ⁇ g/mL (final standard concentration of 30, 15, 10, 6.7, 4.4, 3.0. 1.5, 0.75, and 0.375 ⁇ g/mL) See the following Table 1.
  • the Capture Antibody i.e., mouse anti-human MDC
  • PBS carrier protein
  • the diluted capture antibody was used to coat 96-well plates, and then each plate was sealed and incubated overnight at room temperature. Before using the coated plates, each well was aspirated and washed with Wash Buffer, repeating the process two times for a total of three washes. The plates were then blocked by adding 300 ⁇ L of Reagent Diluent to each well and incubating at room temperature for one hour. After incubation the aspiration and well-washing procedure was repeated.
  • the ELISA assay 100 ⁇ L samples of either the supernatants from the monocyte/fibrocyte cultures or the SAP standards were added to each well. The plate was then incubated at room temperature for 2 hours before aspirating and washing the wells. Then 100 ⁇ L of a working dilution of Streptavidin-HRP was added to each well. The plate was incubated for 20 minutes at room temperature before adding 50 ⁇ L of Stop Solution to each well. Immediately, the optical density of each well was measured using a microplate reader set to 450 nm. If wavelength correction was available, the microplate reader was set to 540 nm or 570 nm. If wavelength correction was not available, then the readings at 540 nm or 570 nm were subtracted from the readings at 450 nm This subtraction corrects for optical imperfections in the plate.
  • Deglycosylated SAP Variants have Altered Plasma Half-Life and Biological Activity
  • wild-type hSAP was treated with a sialidase to remove all sialic acid moieties attached to the SAP polypeptide (i.e., asialo hSAP).
  • Both the untreated rhSAP N32D and asialo hSAP were compared with a corresponding sample of rhSAP in a PK assay to measure for in vivo serum stability ( FIG. 4 ). While the PK of the rhSAP N32D was slightly reduced compared to wild-type SAP, the half-life of the rhSAP N32D was substantially higher than that of the asialo hSAP. The rhSAP N32D variant was further compared to a corresponding sample of serum-derived hSAP using an in vitro bioassay to determine the relative activity of these proteins ( FIG. 3 ). These data indicate that the N32D SAP variant maintains a plasma half-life and activity comparable to wild-type hSAP.
  • a recombinant human SAP (rhSAP) variant was covalently attached to a 20 kDa activated methoxyPEG derivative (PEG).
  • the PEG moiety was attached to a primary amine group of rhSAP according to the following protocol and as illustrated in FIG. 5 .
  • approximately 1 mg of 20 kDa methoxy-PEG-succinimidyl-carboxymethyl ester (JenKem cat#M-SCM-20K) per mg of rhSAP was dissolved in a 20 mg/mL solution of rhSAP.
  • the coupling reaction was allowed to proceed for 24 hours at room temperature.
  • the resulting pegylated-rhSAP was purified from reaction components by anion exchange chromatography.
  • PEGylated rhSAP made by this procedure contained from 1-3 20 kDa PEGs/protomer, with 1 PEG/protomer being the most abundant form, as assessed by SDS-PAGE.
  • the PEGylated rhSAP and human serum-derived SAP (hSAP) were assayed for bioactivity using an in vitro bioassay.
  • monocyte enriched Peripheral Blood Mononuclear Cells (PBMCs) were incubated with varying concentrations of either PEGylated rhSAP or hSAP for 96 hours.
  • PBMCs Peripheral Blood Mononuclear Cells
  • resulting culture supernatants were removed and assayed by ELISA to quantify the amount of Macrophage Derived Chemokine (MDC) that was produced.
  • MDC Macrophage Derived Chemokine
  • the relative potency of a SAP variant can be determined.
  • the result is expressed as an IC 50 ratio of the sample versus the hSAP reference standard as described in the preceding examples.
  • the PEGylated rhSAP variant was had an IC 50 ratio of 0.24 compared to a corresponding sample of hSAP, thereby demonstrating that the PEGylated rhSAP has comparable activity to wild-tvae SAP.

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